1. Field of the Invention
The present invention relates to the field of molecular biology and nucleic acid chemistry. More specifically, it relates to methods and reagents for improving nucleic acid amplification reactions. The invention therefore has applications in any field in which nucleic acid amplification is used.
2. Description of Related Art
The invention of the polymerase chain reaction (PCR) made possible the in vitro amplification of nucleic acid sequences. PCR is described in U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188; Saiki et al., 1985, Science 230:1350-1354; Mullis et al., 1986, Cold Springs Harbor Symp. Quant. Biol. 51:263-273; and Mullis and Faloona, 1987, Methods Enzymol. 155:335-350; each of which is incorporated herein by reference. The development and application of PCR are described extensively in the literature. For example, a range of PCR-related topics are discussed in PCR Technologyxe2x80x94principles and applications for DNA amplification, 1989, (ed. H. A. Erlich) Stockton Press, New York; PCR Protocols: A guide to methods and applications, 1990, (ed. M. A. Innis et al.) Academic Press, San Diego; and PCR Strategies, 1995, (ed. M. A. Innis et al.) Academic Press, San Diego; each of which is incorporated herein by reference. Commercial vendors, such as Applied Biosystems (Foster City, Calif.), market PCR reagents and publish PCR protocols.
Since the original publication of nucleic acid amplification, various primer-based nucleic acid amplification methods have been described including, but not limited to, the strand displacement assay (Walker et al., 1992, Proc. Natl. Acad. Sci. USA 89:392-396, Walker et al. 1992, Nucleic Acids Res. 20:1691-1696, and U.S. Pat. No. 5,455,166) and the transcription-based amplification systems, including the methods described in U.S. Pat. Nos. 5,437,990; 5,409,818; and 5,399,491; the transcription amplification system (TAS) (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177); and self-sustained sequence replication (3SR) (Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878 and WO 92/08800). All of the above references are incorporated herein by reference. A survey of amplification systems is provided in Abramson and Myers, 1993, Current Opinion in Biotechnology 4:41-47, incorporated herein by reference.
Specificity of primer-based amplification reactions largely depends on the specificity of primer hybridization and extension. Under the elevated temperatures used in a typical amplification, the primers hybridize only to the intended target sequence. However, amplification reaction mixtures are typically assembled at room temperature, well below the temperature needed to insure primer hybridization specificity. Under such less stringent conditions, the primers may bind non-specifically to other only partially complementary nucleic acid sequences or to other primers and initiate the synthesis of undesired extension products, which can be amplified along with the target sequence. Amplification of non-specific primer extension products can compete with amplification of the desired target sequences and can significantly decrease the efficiency of the amplification of the desired sequence.
One frequently observed type of non-specific amplification product is a template-independent artifact of amplification reactions referred to as xe2x80x9cprimer dimerxe2x80x9d. Primer dimer is a double-stranded fragment whose length typically is close to the sum of the two primer lengths and appears to occur when one primer is extended over the other primer. The resulting extension product forms an undesired template which, because of its short length, is amplified efficiently.
Non-specific amplification can be reduced by reducing the formation of primer extension products prior to the start of the reaction. In one method, referred to as a xe2x80x9chot-startxe2x80x9d protocol, one or more critical reagents are withheld from the reaction mixture until the temperature is raised sufficiently to provide the necessary hybridization specificity. Manual hot-start methods, in which the reaction tubes are opened after the initial high temperature incubation step and the missing reagents are added, are labor intensive and increase the risk of contamination of the reaction mixture. Alternatively, a heat sensitive material, such as wax, can be used to separate or sequester reaction components, as described in U.S. Pat. No. 5,411,876, incorporated herein by reference, and Chou et al., 1992, Nucl. Acids Res. 20(7):1717-1723, incorporated herein by reference. In these methods, a high temperature pre-reaction incubation melts the heat sensitive material, thereby allowing the reagents to mix.
Another method of reducing the formation of primer extension products prior to the start of the reaction relies on the heat-reversible inactivation of the DNA polymerase. U.S. Pat. Nos. 5,773,258 and 5,677,152, both incorporated herein by reference, describe DNA polymerases reversibly modified by the covalent attachment of a modifier group. Incubation of the inactivated DNA polymerase at high temperature results in cleavage of the modifier-enzyme bond, thereby reactivating the enzyme.
Non-covalent reversible inhibition of a DNA polymerase by DNA polymerase-specific antibodies is described in U.S. Pat. Nos. 5,338,671, incorporated herein by reference.
Non-specific amplification also can be reduced by enzymatically degrading extension products formed prior to the start of the reaction using the methods described in U.S. Pat. No. 5,418,149, which is incorporated herein by reference. The degradation of newly-synthesized extension products is achieved by incorporating into the reaction mixture dUTP and UNG, and incubating the reaction mixture at 45-60xc2x0 C. prior to carrying out the amplification reaction. Primer extension results in the formation of uracil-containing DNA, which is degraded by UNG under the pre-amplification conditions. A disadvantage of this method is that the degradation of extension product competes with the formation of extension product and the elimination of non-specific primer extension product may be less complete. An advantage of this method is that uracil-containing DNA introduced into the reaction mixture as a contamination from a previous reaction is also degraded and, thus, the method also reduces the problem of contamination of a PCR by the amplified nucleic acid from previous reactions.
Another method of reducing the formation of primer extension products prior to the start of the reaction relies on the use of primers modified at or near the 3xe2x80x2 end by the addition of a moiety to an exocyclic amine, as described in U.S. Pat. No. 6,001,611, incorporated herein by reference.
Conventional techniques of molecular biology and nucleic acid chemistry, which are within the skill of the art, are fully explained fully in the literature. See, for example, Sambrook et al., 1989, Molecular Cloningxe2x80x94A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Nucleic Acid Hybridization (B. D. Hames and S. J. Higgins. eds., 1984); PCR Technologyxe2x80x94principles and applications for DNA amplification, 1989, (ed. H. A. Erlich) Stockton Press, New York; PCR Protocols: A guide to methods and applications, 1990, (ed. M. A. Innis et al.) Academic Press, San Diego; and PCR Strategies, 1995, (ed. M. A. Innis et al.) Academic Press, San Diego; all of which are incorporated herein by reference.
The present invention provides methods and reagents for the in vitro amplification of a nucleic acid sequence using a primer-based amplification reaction which provide a simple and economical solution to the problem of non-specific amplification. The methods involve the use of oligonucleotide primers containing particular modifications to the sugar-phosphate backbone at or near the 3xe2x80x2 terminus.
In one embodiment, the methods involve the use of a modified primer consisting essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide selected from the group consisting of 2xe2x80x2-O-methyl-nucleotides, 2xe2x80x2-amino-nucleotides, and 2xe2x80x2-fluoro-nucleotides.
In another embodiment, the methods involve the use of a modified primer consisting essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide that contains arabinose.
One aspect of the invention relates to kits for the in vitro amplification of a nucleic acid sequence using a primer-based amplification reaction, which kits comprise at least one modified primer, preferably two, for each intended target. A kit typically will comprise one or more amplification reagents, e.g., a nucleic acid polymerase, nucleoside triphosphates, or suitable buffers. Optionally, a kit may comprise addition components, such as a means for detecting the amplified product.
Another aspect of the present invention relates to methods for amplifying a nucleic acid which comprise carrying out a primer-based nucleic acid amplification reaction using at least one modified primer. Thus, the present invention provides a method for the amplifying a target nucleic acid contained in a sample, comprising:
(a) providing an amplification reaction mixture comprising the target nucleic acid and a pair of primers, wherein one or both members of the pair of primers are modified primers; and
(b) treating the reaction mixture of step (a) under conditions suitable for the amplification of the nucleic acid.
In a preferred embodiment of the invention, the amplification reaction is a polymerase chain reaction (PCR) wherein at least one and, preferably all, of the primers are modified.
Another aspect of the invention relates to amplification reaction mixtures which contain at least one modified primer. In a preferred embodiment, the amplification reaction mixture contains a pair of modified oligonucleotide primers for carrying out a PCR.
To aid in understanding the invention, several terms are defined below.
The terms xe2x80x9cnucleic acidxe2x80x9d and xe2x80x9coligonucleotidexe2x80x9d refer to polydeoxyribonucleotides (containing 2xe2x80x2-deoxy-D-ribose), to polyribonucleotides (containing D-ribose), and to any other type of polynucleotide which is an N glycoside of a purine or pyrimidine base. There is no intended distinction in length between the terms xe2x80x9cnucleic acidxe2x80x9d and xe2x80x9coligonucleotidexe2x80x9d, and these terms will be used interchangeably. These terms refer only to the primary structure of the molecule. Thus, these terms include double- and single-stranded DNA, as well as double- and single-stranded RNA. For use in the present invention, an oligonucleotide also can comprise non-purine or non-pyrimidine nucleotide analogs.
Oligonucleotides can be prepared by any suitable method, including direct chemical synthesis by a method such as the phosphotriester method of Narang et al., 1979, Meth. Enzymol. 68:90-99; the phosphodiester method of Brown et al., 1979, Meth. Enzymol. 68:109-151; the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett. 22:1859-1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference. A review of synthesis methods of conjugates of oligonucleotides and modified nucleotides is provided in Goodchild, 1990, Bioconjugate Chemistry 1(3):165-187, incorporated herein by reference.
The term xe2x80x9cprimerxe2x80x9d refers to an oligonucleotide capable of acting as a point of initiation of DNA synthesis under conditions in which synthesis of a primer extension product complementary to a nucleic acid strand is induced, i.e., either in the presence of four different nucleoside triphosphates and an agent for extension (e.g., a DNA polymerase or reverse transcriptase) in an appropriate buffer and at a suitable temperature. A primer is preferably a single-stranded DNA. The appropriate length of a primer depends on the intended use of the primer but typically ranges from 10 to 50 nucleotides, preferably from 15-35 nucleotides. Short primer molecules generally require lower temperatures to form sufficiently stable hybrid complexes with the template. A primer need not reflect the exact sequence of the template nucleic acid, but must be sufficiently complementary to hybridize with the template. The design of suitable primers for the amplification of a given target sequence is well known in the art and described in, for example, the literature cited herein.
Primers can incorporate additional features which allow for the detection or immobilization of the primer but do not alter the basic property of the primer, that of acting as a point of initiation of DNA synthesis. For example, primers may contain an additional nucleic acid sequence at the 5xe2x80x2 end which does not hybridize to the target nucleic acid, but which facilitates cloning of the amplified product. The region of the primer which is sufficiently complementary to the template to hybridize is referred to herein as the hybridizing region.
As used herein, a xe2x80x9cmodified primerxe2x80x9d refers to a primer that includes at least one nucleotide containing a sugar other than the conventional 2xe2x80x2-deoxy-D-ribose or D-ribose found in naturally occurring DNA and RNA. Similarly, as used herein, a xe2x80x9cmodified nucleotidexe2x80x9d refers to a nucleotide containing a sugar other than the conventional 2xe2x80x2-deoxy-D-ribose or D-ribose found in naturally occurring DNA and RNA, and encompasses nucleotides in which the sugar is modified by the addition or substitution of a side group, or in which the sugar is a stereoisomer of the conventional 2xe2x80x2-deoxy-D-ribose or D-ribose found in naturally occurring DNA and RNA, or both. The terms are not used to indicate that a modified primer or nucleotide is the product of a process of modification, but rather to indicate the presence of differences in the oligonucleotide backbone relative to naturally occurring DNA or RNA. In particular, the primers of the present invention preferably are synthesized to contain a modified nucleotide, although the chemical modification of a primer initially containing only conventional nucleotides may provide an alternative synthesis.
The terms xe2x80x9ctargetxe2x80x9d, xe2x80x9ctarget sequencexe2x80x9d, xe2x80x9ctarget regionxe2x80x9d, and xe2x80x9ctarget nucleic acidxe2x80x9d refer to a region or subsequence of a nucleic acid which is to be amplified.
The term xe2x80x9chybridizationxe2x80x9d refers the formation of a duplex structure by two single-stranded nucleic acids due to complementary base pairing. Hybridization can occur between fully complementary nucleic acid strands or between xe2x80x9csubstantially complementaryxe2x80x9d nucleic acid strands that contain minor regions of mismatch. Conditions under which only fully complementary nucleic acid strands will hybridize are referred to as xe2x80x9cstringent hybridization conditionsxe2x80x9d or xe2x80x9csequence-specific hybridization conditionsxe2x80x9d. Stable duplexes of substantially complementary sequences can be achieved under less stringent hybridization conditions; the degree of mismatch tolerated can be controlled by suitable adjustment of the hybridization conditions. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length and base pair concentration of the oligonucleotides, ionic strength, metal cation, and incidence of mismatched base pairs, following the guidance provided by the art (see, e.g., Sambrook et al., 1989, Molecular Cloningxe2x80x94A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; and Wetmur, 1991, Critical Review in Biochem. and Mol. Biol. 26(3/4):227-259; both incorporated herein by reference).
As used herein, a primer is xe2x80x9cspecificxe2x80x9d for a target sequence if, when used in an amplification reaction under sufficiently stringent conditions, the primer can be extended only if hybridized to the target nucleic acid. Typically, a primer is specific for a target sequence if the primer-target duplex stability, particularly in the region of the 3xe2x80x2 terminus of the primer, is greater than the stability of a duplex formed between the primer and any other sequence found in the sample. One of skill in the art will recognize that various factors, such as base composition of the primer and the location of the mismatches, will affect the specificity of the primer, and that routine experimental confirmation of the primer specificity will be needed in most cases. Hybridization conditions under which a target-specific primer will be extendable only if hybridized with a target sequence can be determined empirically in a routine manner. Thus, the use of target-specific primers under suitably stringent amplification conditions enables the specific amplification of those target sequences which contain the target primer binding sites. The use of sequence-specific amplification conditions enables the specific amplification of those target sequences which contain the exactly complementary primer binding sites.
The term xe2x80x9cnon-specific amplificationxe2x80x9d refers to the amplification of nucleic acid sequences other than the target sequence which results from primers hybridizing to sequences other than the target sequence and then serving as a substrate for primer extension. The hybridization of a primer to a non-target sequence is referred to as xe2x80x9cnon-specific hybridizationxe2x80x9d and can occur during the lower temperature, reduced stringency, pre-amplification conditions. One of skill in the art will understand that even highly unstable duplexes, although highly disfavored in an equilibrium state, may form transiently.
The term xe2x80x9cprimer dimerxe2x80x9d is used herein generically to encompasses template-independent non-specific amplification product. Primer dimer is believed to result from primer extensions wherein another primer serves as a template, although the genesis of primer dimer is not well understood. The resulting amplification product typically appears to correspond approximately to a concatamer of two primers, i.e., a dimer, although concatamers of more than two primers also occur.
The term xe2x80x9creaction mixturexe2x80x9d refers to a solution containing reagents necessary to carry out a given reaction. An xe2x80x9camplification reaction mixturexe2x80x9d, which refers to a solution containing reagents necessary to carry out an amplification reaction, typically contains oligonucleotide primers and a nucleic acid polymerase in a suitable buffer. A xe2x80x9cPCR reaction mixturexe2x80x9d typically contains oligonucleotide primers, a DNA polymerase (most typically a thermostable DNA polymerase), dNTP""s, and a divalent metal cation in a suitable buffer. A reaction mixture is referred to as complete if it contains all reagents necessary to enable the reaction, and incomplete if it contains only a subset of the necessary reagents. It will be understood by one of skill in the art that reaction components are routinely stored as separate solutions, each containing a subset of the total components, for reasons of convenience, storage stability, or to allow for application-dependent adjustment of the component concentrations, and that reaction components are combined prior to the reaction to create a complete reaction mixture. Furthermore, it will be understood by one of skill in the art that reaction components are packaged separately for commercialization and that useful commercial kits of the invention may contain any subset of the reaction components which includes the modified primers of the invention.
All patents, patent applications, and publications cited herein, both supra and infra, are incorporated herein by reference.
Modified Primers
The modified amplification primers of the present invention contain particular modifications to the sugar-phosphate backbone at or near the 3xe2x80x2 terminus. In one embodiment, the modified primers consist essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide selected from the group consisting of 2xe2x80x2-O-methyl-nucleotides, 2xe2x80x2-amino-nucleotides, and 2xe2x80x2-fluoro-nucleotides. In a preferred embodiment, the modified primers consist essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide selected from the group consisting of 2xe2x80x2-O-methyl-ribonucleotides, 2xe2x80x2-deoxy-2xe2x80x2-amino-nucleotides, and 2xe2x80x2-deoxy-2xe2x80x2-fluoro-nucleotides. These modifications represent the addition of a moiety to the 2xe2x80x2 OH, or the replacement of the 2xe2x80x2 OH by an alternative moiety.
In another embodiment, the modified primer consists essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide that contains arabinose. Arabinose is a stereoisomer of ribose that differs only in the configuration about C-2. It is expected that embodiments in which 2xe2x80x2position of the arabinose is modified by the addition of a moiety to the 2xe2x80x2 OH or replacement of the 2xe2x80x2-OH by an alternative moiety will be useful in the methods of the present invention. In a preferred embodiment, the modified primer consists essentially of an oligonucleotide in which at least one of the three 3xe2x80x2 terminal nucleotides is a modified nucleotide that contains an unmodified arabinose.
The design and use of amplification primers in general is well known in the art. The primers of the present invention are distinguished by the inclusion of the specified modified nucleotides in the primer sequence. Other aspects of the primer, such as the overall length and sequence, are selected following the standard practice of primer design.
Typically, primers consist of a single strand of deoxyribonucleotides (DNA) and contain the conventional bases: the two purine bases, adenine and guanine, and the two pyrimidine bases, cytosine and thymine. However, the present invention is not limited to primers consisting only of the conventional bases. Base analogs may be used, for example, to alter the hybridization stability of the primer-target duplex. Any base analog which can be used in an unmodified amplification primer can be used in the primers of the present invention. Examples of base analogs, also referred to as unconventional bases, include 3-methyladenine, 7-methylguanine, 3-methylguanine, 5-methyl cytosine, and 5-hydroxymethyl cytosine.
Theory of Operation
A primer-based amplification involves repeated primer extensions in which the primers first hybridize to target nucleic acid and then are enzymatically extended. The specificity of the amplification depends on the specificity of the primer hybridization. One hypothesis is that non-specific amplification occurs when an unstable, transient hybridization duplex is formed between a primer and a non-target molecule, possibly another primer, in which the 3xe2x80x2 end of the primer is momentarily paired with a complementary base in the other molecule. Initial primer extension results in the formation of complementary sequence which stabilizes the duplex and allows further extension.
While not being constrained by the theory, it is believed that the modified primers of the present invention reduce non-specific amplification by increasing the time required for the initial primer extension to occur. The backbone modifications probably delay the initial extension by rendering the primer-target duplex a less preferred template for extension. The delay in the initial extension reduces the likelihood that an unstable, transient hybridization duplex, such as between primers under pre-reaction conditions, will exist for a sufficient time to permit primer extension.
In contrast, primer-target hybridization duplexes are sufficiently stable under the primer hybridization condition used in an amplification such that the additional time required does not hinder extension. Thus, under this model, the modification does not significantly inhibit primer extension under the amplification conditions, but does decrease the probability of extension of primers involved in unstable, transient duplexes formed with non-target sequences under the pre-amplification conditions.
The 2xe2x80x2-O-methyl-ribonucleotides, 2xe2x80x2-deoxy-2xe2x80x2-amino-nucleotides, and 2xe2x80x2-deoxy-2xe2x80x2-fluoro-nucleotides, relative to a typical oligodeoxynucleotide primer, contain bulkier side groups bound to C-2 of the sugar. It is likely that the side group sterically interferes with the binding of the enzyme to the primer-target duplex, but not enough to preclude extension. This suggests that additional side groups of similar bulk would have a similar effect and also could be used in the methods of the invention.
The arabinose-containing nucleotides, by changing the orientation of the H and OH side groups bound to the C-2 of the sugar, alter the interaction with the enzyme. It is likely that other stereoisomers may inhibit, but not preclude, extension, and these compounds are expected to be useful in the methods of the invention.
Synthesis of Modified Primers
Synthesis of the modified primers is carried out using standard chemical means well known in the art, for example, the diethylphosphoramidite method of Beaucage et al., 1981, Tetrahedron Lett. 22:1859-1862; and the solid support method of U.S. Pat. No. 4,458,066, each incorporated herein by reference.
Preferably, the synthesis reaction is carried out in a commercially available automatic DNA synthesizer (e.g., ABI 374 DNA synthesizer from Applied Biosystems, Foster City, Calif.) using commercially available nucleotide phosphoramidites (e.g., from Applied Biosystems, Foster City, Calif.). Nucleotide phosphoramidites and supports suitable for synthesizing oligonucleotides containing modified nucleotides as used herein are commercially available from, for example, Glen Research (Sterling, Va.).
Standard oligonucleotide synthesis is carried out by the stepwise addition of nucleoside monomers to a growing chain. Each addition involves the coupling of a reactive 3xe2x80x2 phosphorous group of a nucleoside monomer to the 5xe2x80x2 hydroxyl of another nucleoside bound to a solid support. After addition of the final nucleoside, the oligonucleotide is cleaved from the support, protecting groups are removed from the bases, and the oligonucleotide is purified for use.
Using standard synthesis methods, 3xe2x80x2 terminal nucleotide in the final oligonucleotide is derived from the nucleoside initially bound to the solid support. Thus, synthesis of oligonucleotides containing a 3xe2x80x2 terminal modified nucleotide is carried out starting with a solid support containing the modified nucleoside. Synthesis of oligonucleotides containing an internal modified nucleotide is carried out using the appropriate nucleoside phosphoramidite monomers.
The 2xe2x80x2-O-methylribonuclesides are commercially available both as phosphoramidites and pre-attached to a synthesis support. Other modified nucleotides may be readily available only as phosphoramidites. Alternative synthesis supports are available that enable the synthesis of oligonucleotides with a 3xe2x80x2 terminal modified nucleotide using the phosphoramidites of the modified nucleoside monomers. For example, universal supports, such as marketed by Glen Research (Sterling, Va.) under license from Avecia Ltd., allow cleavage of the synthesized oligonucleotide from the solid support between the first and second 3xe2x80x2 monomers. A modified nucleoside destined to become the 3xe2x80x2 terminal nucleoside is added in the first monomer addition and, thus, becomes the second monomer in the growing chain. Following the final addition, the 3xe2x80x2 terminal nucleoside, originally attached to the support, is eliminated during the final cleavage step, leaving the desired terminal-modified nucleotide.
Amplifications Using Modified Primers
The methods of the present invention comprise carrying out a primer-based amplification, wherein at least one of the primers is a modified primer of the present invention. In general, the modified primers can be substituted for unmodified primers containing the same nucleotide sequence in a primer-based amplification with only routine modifications in the amplification reaction conditions following the guidance herein.
In a preferred embodiment, the modified primers of the present invention are used in the polymerase chain reaction (PCR), described in U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188; Saiki et al., 1985, Science 230:1350-1354; Mullis et al., 1986, Cold Springs Harbor Symp. Quant. Biol. 51:263-273; and Mullis and Faloona, 1987, Methods Enzymol. 155:335-350; each of which is incorporated herein by reference. However, the invention is not restricted to any particular amplification system. The use of the modified primers in other primer-based amplification methods in which primer dimer or non-specific amplification product can be formed is expected to be useful. Examples of primer-based amplification methods include the strand displacement assay (Walker et al., 1992, Proc. Natl. Acad. Sci. USA 89:392-396, Walker et al. 1992, Nucleic Acids Res. 20:1691-1696, and U.S. Pat. No. 5,455,166) and the transcription-based amplification methods, including the methods described in U.S. Pat. Nos. 5,437,990; 5,409,818; and 5,399,491; the transcription amplification system (TAS) (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177); and self-sustained sequence replication (3SR) (Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878 and WO 92/08800). All of the above references are incorporated herein by reference. A survey of amplification systems is provided in Abramson and Myers, 1993, Current Opinion in Biotechnology 4:41-47, incorporated herein by reference.
Enzymes for use in the nucleic acid amplification methods described above are well known in the art. For example, DNA polymerases and mutants thereof useful for various applications of PCR are described in U.S. Pat. Nos. 4,889,818; U.S. Pat. No. 5,079,352; U.S. Pat. No. 5,352,600; U.S. Pat. No. 5,374,553; U.S. Pat. No. 5,405,774; U.S. Pat. No. 5,420,029; U.S. Pat. No. 5,455,170; U.S. Pat. No. 5,466,591; U.S. Pat. No. 5,491,086; U.S. Pat. No. 5,618,711; U.S. Pat. No. 5,624,833; U.S. Pat. No. 5,674,738; U.S. Pat. No. 5,677,152; U.S. Pat. No. 5,773,258; U.S. Pat. No. 5,789,224; U.S. Pat. No. 5,795,762; U.S. Pat. No. 5,939,292; U.S. Pat. No. 5,968,799; European patent publication No. 892,058; European patent publication No. 823,479; European Patent Publication No. 0 902,035; and co-pending U.S. application Ser. No. 09/146,631, each incorporated herein by reference. Additional enzymes for use in other nucleic acid amplification methods also are well known in the art and described in, for example, the references cited above which describe the amplification methods.
One of skill in the art will understand that the magnitude of the effect of the modified primers will depend on the particular amplification reaction and reaction conditions selected. The magnitude of the effect can be determined empirically, following the teaching in the examples.
DNA polymerases require a divalent cation for catalytic activity. For extension reactions using a thermoactive or thermostable DNA polymerase and a DNA template, the preferred divalent cation is Mg+2, although other cations, such as Mn+2 or Co+2 can activate DNA polymerases. The use of Mn+2 to increase the efficiency of extension reactions using an RNA template, i.e., reverse-transcription, is described in U.S. Pat. No. 5,310,652; U.S. Pat. No. 5,322,770; U.S. Pat. No. 5,407,800; U.S. Pat. No. 5,561,058; U.S. Pat. No. 5,641,864; and U.S. Pat. No. 5,693,517; all incorporated herein by reference. The use of Mn+2 also decreases the fidelity of amplifications, either using an RNA or a DNA template. In general, the use of Mn+2 decreases the delay of the template amplification resulting from the use of the modified primers when compared to an amplification carried out using Mg+2.
Particular mutant DNA polymerases may be useful in the present invention. Co-pending U.S. application Ser. No. 60/198,336, incorporated herein by reference, describes the use of particular mutant DNA polymerases, which are described in European Patent Publication No. 0 902,035 and co-pending U.S. application Ser. No. 09/146,631, both incorporated herein by reference, to achieve more efficient high-temperature reverse-transcription and RNA amplification reactions, particularly in Mg+2-activated reactions. As described in the examples, this particular mutation tends to decrease the delaying effect of the modified primers on target amplification when used in the methods of the present invention. DNA polymerases derived from Thermatoga maritima, described in patents cited above, may provide similar advantages when used in the present methods.
The selection of suitable primer modifications, enzymes, cation, and other reaction reagents and conditions will depend on the application. In some application, the minimization of primer dimer may be more important than the target amplification efficiency. In other applications, it may be desirable to maintain target amplification efficiency as much as possible while decreasing primer dimer. One of skill will understand that suitable reaction conditions in general, and the enzyme and divalent cation in particular, can be selected empirically for any particular application using routine experimental methods, following the guidance herein and in the examples.
The present invention is compatible with other methods of reducing non-specific amplification, such as those described in the references cited supra. For example, the present invention can be used in an amplification carried out using a reversibly inactivated enzyme as described in U.S. Pat. Nos. 5,677,152, and 5,773,258, each incorporated herein by reference. The use of a reversibly inactivated enzyme, which is re-activated under the high temperature reaction conditions, further reduces non-specific amplification by inhibiting primer extension of any modified primers prior to the start of the reaction. A reversibly inactivated thermostable DNA polymerase, developed and manufactured by Hoffman-La Roche (Nutley, N.J.) and marketed by Applied Biosystems (Foster City, Calif.), is described in Birch et al., 1996, Nature 381(6581):445-446, incorporated herein by reference.
The present invention also can be used in conjunction with the modified primers described in U.S. Pat. No. 6,001,611, incorporated herein by reference. As described therein, primers can be modified by the covalent attachment of a modifier group to the exocyclic amine of a nucleotide at or near the 3xe2x80x2 terminus. The attachment of a group to the exocyclic amine does not interfere with the use of modified nucleotides at or near the 3xe2x80x2 terminus, as specified herein. Suitable combinations of primer modifications for use with a particular target and reaction conditions can be selected by routine experimentation as described in the examples, below.
Sample preparation methods suitable for amplification reactions are well known in the art and fully described in the literature cited herein. The particular method used is not a critical part of the present invention. One of skill in the art can optimize reaction conditions for use with the known sample preparation methods.
Methods of analyzing amplified nucleic acid are well known in the art and fully described in the literature cited herein. The particular method used is not a critical part of the present invention. One of skill in the art can select a suitable analysis method depending on the application.
A preferred method for analyzing an amplification reaction is by monitoring the increase in the total amount of double-stranded DNA in the reaction mixture, as described in Higuchi et al., 1992, Bio/Technology 10:413-417; Higuchi et al., 1993, Bio/Technology 11:1026-1030; Higuchi and Watson, 1999, in PCR Applications (Innis et al., eds.) Chapter 16, Academic Press, San Diego; U.S. Pat. No. 5,994,056; and European Patent Publication Nos. 487,218 and 512,334, each incorporated herein by reference. In this method, referred to herein as xe2x80x9ckinetic PCRxe2x80x9d, the detection of double-stranded DNA relies on the increased fluorescence that ethidium bromide (EtBr) and other DNA binding labels exhibit when bound to double-stranded DNA. The amplification is carried out in the presence of the label. The increase of double-stranded DNA resulting from the synthesis of target sequences results in an increase in the amount of label bound to double-stranded DNA and a concomitant detectable increase in fluorescence, which is monitored during the amplification. Thus, the methods enable monitoring the progress of an amplification reaction.
In a kinetic PCR, the measured fluorescence depends on the total amount of double-stranded DNA present, whether resulting from non-specific amplification or from amplification of the target sequence. Monitoring the fluorescence allows measurement of the increase in the total amount of double-stranded DNA is measured, but the increase resulting from amplification of the target sequence is not measured independently from the increase resulting from non-specific amplification product. The modified primers of the present invention are particularly useful in kinetic PCR because they not only reduce the amount of primer dimer formed, but also delay the formation of detectable amounts of primer dimer. A delay of primer dimer formation until after a significant increase in target sequence has occurred enables independent monitoring of the amplification of target sequences and minimizes the interference from primer dimer.
Kits
The present invention also relates to kits, typically multi-container units comprising useful components for practicing the present method. A useful kit contains primers, at least one of which is modified as described herein, for nucleic acid amplification. Other optional components of the kit include, for example, an agent to catalyze the synthesis of primer extension products, the substrate nucleoside triphosphates, appropriate reaction buffers, and instructions for carrying out the present method.
The examples of the present invention presented below are provided only for illustrative purposes and not to limit the scope of the invention. Numerous embodiments of the invention within the scope of the claims that follow the examples will be apparent to those of ordinary skill in the art from reading the foregoing text and following examples.